Well the mainshaft snout helps align the input shaft. The way it rests on the main shaft there is a set of bearings that help align it and keep it axially aligned. The input retainer keeps preload on the main shaft and radial alignment.
Here is a
manual for the T-5. It isn't that bad. Perhaps something was unintentionally moved when you replaced the retainer the first time. Look it over. Go to section 6 page 6. This is where the input shaft assembly is best viewed.
If something was lost it is recoverable. You can replace what was lost and reinstall it.
I work on alot of T-5's but I haven't seen everything. I hope we are on the right track.
Mike